Dy-SheHeRASADe: A representation of the β sheet dynamics through surface descriptors.

Molecular dynamics (MD) simulations are important tools for studying the dynamic motions of macromolecules at the atomic level. With the increasing capabilities of high performance computing, MD simulations are becoming more widely used. This allows molecular modelers to simulate the molecular behavior of large molecular architectures for much longer trajectories.

Challenging level of rigid-body approach involving numerical elements (CHLORAINE) applied to repeated elastin peptides.

Elastic proteins and derived biomaterials contain numerous tandemly repeated peptides along their sequences, ranging from a few copies to hundreds. These repetitions are responsible for their biochemical, biological and biomechanical properties. These sequences are considered to be intrinsically disordered, and the variations in their behavior are actually mainly due to their high flexibility and lack of stable secondary structures originating from their unique amino acid sequences.

Modelling and Simulations of Extracellular Glycoproteins.

While the knowledge of protein structure and function has seen vast advances in previous decades, the understanding of how their posttranslational modifications, such as glycosylations, influence their structure and function remains poor. However, advances in in silico methodologies to study glycosylations in recent past have enabled us to study this and understand the role of glycosylations in protein structure and function in ways that would not be possible by conventional experimental methods. In this chapter, we will demonstrate how to leverage these methodologies to study glycoproteins and their structural and dynamic properties using molecular modelling techniques.

Multiscale modelling of the extracellular matrix.

The extracellular matrix is a complex three-dimensional network of molecules that provides cells with a complex microenvironment. The major constituents of the extracellular matrix such as collagen, elastin and associated proteins form supramolecular assemblies contributing to its physicochemical properties and organization. The structure of proteins and their supramolecular assemblies such as fibrils have been studied at the atomic level (e.

Sitosterol and glucosylceramide cooperative transversal and lateral uneven distribution in plant membranes.

The properties of biomembranes depend on the presence, local structure and relative distribution assumed by the thousands of components it is made of. As for animal cells, plant membranes have been demonstrated to be organized in subdomains with different persistence lengths and times. In plant cells, sitosterol has been demonstrated to confer to phospholipid membranes a more ordered structure while among lipids, glycosphingolipids are claimed to form rafts where they tightly pack with sterols.

LIMONADA: A database dedicated to the simulation of biological membranes.

Cellular membranes are composed of a wide diversity of lipid species in varying proportions and these compositions are representative of the organism, cellular type and organelle to which they belong. Because models of these molecular systems simulated by MD steadily gain in size and complexity, they are increasingly representative of specific compositions and behaviors of biological membranes. Due to the number of lipid species involved, of force fields and topologies and because of the complexity of membrane objects that have been simulated, LIMONADA has been developed as an open database allowing to handle the various aspects of lipid membrane simulation.

Blending Ferulic Acid Derivatives and Polylactic Acid into Biobased and Transparent Elastomeric Materials with Shape Memory Properties.

Thanks to its remarkable properties such as sustainability, compostability, biocompatibility, and transparency, poly-l-lactic acid (PLA) would be a suitable replacement for oil-based polymers should it not suffer from low flexibility and poor toughness, restricting its use to rigid plastic by excluding elastomeric applications. Indeed, there are few fully biobased and biodegradable transparent elastomers-PLA-based or not-currently available. In the last decades, many strategies have been investigated to soften PLA and enhance its toughness and elongation at break by using plasticizers, oligomers, or polymers.

The KIFC1 Kinesin Ensures the Fast Antibody Clearance Required for Parasite Infectivity.

Human innate immunity to involves the trypanosome C-terminal kinesin KIFC1, which transports internalized trypanolytic factor apolipoprotein L1 (APOL1) within the parasite. We show that KIFC1 preferentially associates with cholesterol-containing membranes and is indispensable for mammalian infectivity. Knockdown of KIFC1 did not affect trypanosome growth but rendered the parasites unable to infect mice unless antibody synthesis was compromised.

Structural Analysis of Nonapeptides Derived from Elastin.

Elastin-derived peptides are released from the extracellular matrix remodeling by numerous proteases and seem to regulate many biological processes, notably cancer progression. The canonical elastin peptide is VGVAPG, which harbors the XGXXPG consensus pattern, allowing interaction with the elastin receptor complex located at the surface of cells. Besides these elastokines, another class of peptides has been identified.

Molecular Model for the Self-Assembly of the Cyclic Lipodepsipeptide Pseudodesmin A.

Self-assembly of peptides into supramolecular structures represents an active field of research with potential applications ranging from material science to medicine. Their study typically involves the application of a large toolbox of spectroscopic and imaging techniques. However, quite often, the structural aspects remain underexposed.

Multiple C2 domains and transmembrane region proteins (MCTPs) tether membranes at plasmodesmata.

In eukaryotes, membrane contact sites (MCS) allow direct communication between organelles. Plants have evolved a unique type of MCS, inside intercellular pores, the plasmodesmata, where endoplasmic reticulum (ER)-plasma membrane (PM) contacts coincide with regulation of cell-to-cell signalling. The molecular mechanism and function of membrane tethering within plasmodesmata remain unknown.

Low-diluted Phenacetinum disrupted the melanoma cancer cell migration.

Dynamic and reciprocal interactions generated by the communication between tumor cells and their matrix microenvironment, play a major role in the progression of a tumor. Indeed, the adhesion of specific sites to matrix components, associated with the repeated and coordinated formation of membrane protrusions, allow tumor cells to move along a determined pathway. Our study analyzed the mechanism of action of low-diluted Phenacetinum on murine cutaneous melanoma process in a fibronectin matrix environment.

Linoleic and linolenic acid hydroperoxides interact differentially with biomimetic plant membranes in a lipid specific manner.

Linoleic and linolenic acid hydroperoxides (HPOs) constitute key intermediate oxylipins playing an important role as signaling molecules during plant defense processes in response to biotic or abiotic stress. They have also been demonstrated in vitro as antimicrobial agents against plant fungi and bacteria. To reach the phytopathogens in vivo, the HPOs biosynthesized in the plant cells must cross the plant plasma membrane (PPM) where they can also interact with plasma membrane lipids and have an effect on their organization.

Homology modeling and in vivo functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase.

The P1B ATPase heavy metal ATPase 4 (HMA4) is responsible for zinc and cadmium translocation from roots to shoots in Arabidopsis thaliana. It couples ATP hydrolysis to cytosolic domain movements, enabling metal transport across the membrane. The detailed mechanism of metal permeation by HMA4 through the membrane remains elusive.

Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study.

By manipulating the various physicochemical properties of amino acids, the design of peptides with specific self-assembling properties has been emerging for more than a decade. In this context, short peptides possessing detergent properties (so-called "peptergents") have been developed to self-assemble into well-ordered nanostructures that can stabilize membrane proteins for crystallization. In this study, the peptide with "peptergency" properties, called ADA8 and extensively described by Tao et al.

Interaction between the barley allelochemical compounds gramine and hordenine and artificial lipid bilayers mimicking the plant plasma membrane.

Some plants affect the development of neighbouring plants by releasing secondary metabolites into their environment. This phenomenon is known as allelopathy and is a potential tool for weed management within the framework of sustainable agriculture. While many studies have investigated the mode of action of various allelochemicals (molecules emitted by allelopathic plants), little attention has been paid to their initial contact with the plant plasma membrane (PPM).

Membrane Interactions of Natural Cyclic Lipodepsipeptides of the Viscosin Group.

Many Pseudomonas spp. produce cyclic lipodepsipeptides (CLPs), which, besides their role in biological functions such as motility, biofilm formation and interspecies interactions, are antimicrobial. It has been established that interaction with the cellular membrane is central to the mode of action of CLPs.

Molecular dynamics study of micelles properties according to their size.

Surfactants are molecules able to spontaneously self-assemble to form aggregates with well-defined properties, such as spherical micelles, planar bilayers, cylindrical micelles or vesicles. Micelles have notably several applications in many domains, such as drug delivery or membrane protein solubilization. In this context, the study of micelle formation in relation with the structural and physico-chemical properties of surfactants is of great interest to better control their use in the different application fields.

Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review.

Plasma membranes are complex entities common to all living cells. The basic principle of their organization appears very simple, but they are actually of high complexity and represent very dynamic structures. The interactions between bioactive molecules and lipids are important for numerous processes, from drug bioavailability to viral fusion.

Mechanism of Trypanosoma brucei gambiense resistance to human serum.

The African parasite Trypanosoma brucei gambiense accounts for 97% of human sleeping sickness cases. T. b.

SAHBNET, an accessible surface-based elastic network: an application to membrane protein.

Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network.